1. Login to `transit.uppmax.uu.se` Documentation: - https://www.uppmax.uu.se/support/user-guides/transit-user-guide/ - https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server 2. Mount the `wharf` of your project. ```bash user@transit:~$ mount_wharf sens2023531 Mounting wharf (accessible for you only) to /home/<user>/sens2023531 <user>-sens2023531@bianca-sftp.uppmax.uu.se's password: ``` 4. Navigate to your `wharf` folder 5. Disable Singularity cache ```bash export SINGULARITY_DISABLE_CACHE=true export APPTAINER_DISABLE_CACHE=true unset NXF_SINGULARITY_CACHEDIR ``` 5. Load nf-core software module ```bash module load uppmax bioinfo-tools nf-core/latest Nextflow/latest ``` 7. Run `nf-core` to download the pipeline. ```bash nf-core download pixelator ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.11.1 - https://nf-co.re WARNING Could not find GitHub authentication token. Some API requests may fail. ? Select release / branch: 1.0.2 [release] ? Include the nf-core's default institutional configuration files into the download? Yes In addition to the pipeline code, this tool can download software containers. ? Download software container images: singularity Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote Singularity images are stored. This allows downloaded images to be cached in a central location. ? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file. This is not recommended when downloading Singularity images, as it can take a long time and saves very little space. ? Choose compression type: none INFO Saving 'nf-core/pixelator' Pipeline revision: '1.0.2' Use containers: 'singularity' Container library: 'quay.io' Output directory: 'nf-core-pixelator_1.0.2' Include default institutional configuration: 'True' INFO Downloading centralised configs from GitHub INFO Downloading workflow files from GitHub INFO Processing workflow revision 1.0.2, found 4 container images in total. Downloading singularity images ???????????????????????????????????????????????????????????????????????????????? 100% ? 4/4 completed ``` 8. Running on Bianca ```bash module load bioinfo-tools Nextflow nextflow run ... -profile uppmax --project sens-XXXX-XX .... ``` Note: you might need `-c configs/conf/uppmax.config`, make sure you have the file (it is an option to download it during the pipeline download process). ## Contacts: - [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425) - [UPPMAX](https://www.uppmax.uu.se/) - [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ) ![](https://live.webb.uu.se/digitalAssets/207/c_207717-l_3-k_bg-city.png) ###### tags: `UPPMAX`